On Fri, Nov 2, 2018 at 12:54 PM Lawrence Mitchell <wence@gmx.li> wrote:
On 2 Nov 2018, at 01:37, Matthew Knepley <knepley@gmail.com> wrote:
Well crap. h5py failed, and it does not look like a simple env fix. It is complaining about an SSL certificate. Is there a way to point to something that uses HTTP?
Hmmph, this is very odd. Because that failed checking the certificate for a host it had previously downloaded from (and passed the certificate checks).
This failed at a state late enough in the game that we can try building "in place" in the virtualenv:
$ . firedrake/bin/activate $ cd firedrake/src/h5py $ export CC=mpicc # I assume you got PETSc to build hdf5 $ export HDF5_DIR=$PETSC_DIR/$PETSC_ARCH $ export HDF5_MPI=ON $ pip install .
Okay, this line pip install . fails with (firedrake) firedrake:/PETSc3/fem/firedrake/src/h5py$ pip install . Processing /PETSc3/fem/firedrake/src/h5py Complete output from command python setup.py egg_info: Download error on https://pypi.org/simple/pkgconfig/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:833) -- Some packages may not be found! Couldn't find index page for 'pkgconfig' (maybe misspelled?) Download error on https://pypi.org/simple/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:833) -- Some packages may not be found! No local packages or working download links found for pkgconfig Traceback (most recent call last): File "<string>", line 1, in <module> File "/private/var/folders/hk/tc1pd0g57l78rpt0lttc1sfh0000gn/T/pip-req-build-vy7d9wuj/setup.py", line 168, in <module> cmdclass = CMDCLASS, File "/PETSc3/fem/firedrake/lib/python3.6/site-packages/setuptools/__init__.py", line 139, in setup _install_setup_requires(attrs) File "/PETSc3/fem/firedrake/lib/python3.6/site-packages/setuptools/__init__.py", line 134, in _install_setup_requires dist.fetch_build_eggs(dist.setup_requires) File "/PETSc3/fem/firedrake/lib/python3.6/site-packages/setuptools/dist.py", line 514, in fetch_build_eggs replace_conflicting=True, File "/PETSc3/fem/firedrake/lib/python3.6/site-packages/pkg_resources/__init__.py", line 777, in resolve replace_conflicting=replace_conflicting File "/PETSc3/fem/firedrake/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1060, in best_match return self.obtain(req, installer) File "/PETSc3/fem/firedrake/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1072, in obtain return installer(requirement) File "/PETSc3/fem/firedrake/lib/python3.6/site-packages/setuptools/dist.py", line 581, in fetch_build_egg return cmd.easy_install(req) File "/PETSc3/fem/firedrake/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 670, in easy_install raise DistutilsError(msg) distutils.errors.DistutilsError: Could not find suitable distribution for Requirement.parse('pkgconfig') ---------------------------------------- Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/hk/tc1pd0g57l78rpt0lttc1sfh0000gn/T/pip-req-build-vy7d9wuj/ but I messed it up initially using pip install h5py which succeeds with (firedrake) 1firedrake:/PETSc3/fem/firedrake/src/h5py$ pip install h5py Collecting h5py Downloading https://files.pythonhosted.org/packages/44/81/50a0560aac57a33c2a624d9e160735... (6.0MB) 100% |████████████████████████████████| 6.1MB 677kB/s Requirement already satisfied: six in /PETSc3/fem/firedrake/lib/python3.6/site-packages (from h5py) (1.11.0) Requirement already satisfied: numpy>=1.7 in /PETSc3/fem/firedrake/lib/python3.6/site-packages (from h5py) (1.15.3) Installing collected packages: h5py Successfully installed h5py-2.8.0 Can I keep going from here? How do I restart the Firedrake install? Thanks, Matt
Lawrence
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>